1 |
#include <iostream> |
2 |
#include <cstdlib> |
3 |
|
4 |
#ifdef IS_MPI |
5 |
#include "mpiSimulation.hpp" |
6 |
#include <unistd.h> |
7 |
#endif //is_mpi |
8 |
|
9 |
#include "Integrator.hpp" |
10 |
#include "simError.h" |
11 |
|
12 |
|
13 |
Integrator::Integrator( SimInfo* theInfo, ForceFields* the_ff ){ |
14 |
|
15 |
info = theInfo; |
16 |
myFF = the_ff; |
17 |
isFirst = 1; |
18 |
|
19 |
molecules = info->molecules; |
20 |
nMols = info->n_mol; |
21 |
|
22 |
// give a little love back to the SimInfo object |
23 |
|
24 |
if( info->the_integrator != NULL ) delete info->the_integrator; |
25 |
info->the_integrator = this; |
26 |
|
27 |
nAtoms = info->n_atoms; |
28 |
|
29 |
// check for constraints |
30 |
|
31 |
constrainedA = NULL; |
32 |
constrainedB = NULL; |
33 |
constrainedDsqr = NULL; |
34 |
moving = NULL; |
35 |
moved = NULL; |
36 |
prePos = NULL; |
37 |
|
38 |
nConstrained = 0; |
39 |
|
40 |
checkConstraints(); |
41 |
} |
42 |
|
43 |
Integrator::~Integrator() { |
44 |
|
45 |
if( nConstrained ){ |
46 |
delete[] constrainedA; |
47 |
delete[] constrainedB; |
48 |
delete[] constrainedDsqr; |
49 |
delete[] moving; |
50 |
delete[] moved; |
51 |
delete[] prePos; |
52 |
} |
53 |
|
54 |
} |
55 |
|
56 |
void Integrator::checkConstraints( void ){ |
57 |
|
58 |
|
59 |
isConstrained = 0; |
60 |
|
61 |
Constraint *temp_con; |
62 |
Constraint *dummy_plug; |
63 |
temp_con = new Constraint[info->n_SRI]; |
64 |
nConstrained = 0; |
65 |
int constrained = 0; |
66 |
|
67 |
SRI** theArray; |
68 |
for(int i = 0; i < nMols; i++){ |
69 |
|
70 |
theArray = (SRI**) molecules[i].getMyBonds(); |
71 |
for(int j=0; j<molecules[i].getNBonds(); j++){ |
72 |
|
73 |
constrained = theArray[j]->is_constrained(); |
74 |
|
75 |
if(constrained){ |
76 |
|
77 |
dummy_plug = theArray[j]->get_constraint(); |
78 |
temp_con[nConstrained].set_a( dummy_plug->get_a() ); |
79 |
temp_con[nConstrained].set_b( dummy_plug->get_b() ); |
80 |
temp_con[nConstrained].set_dsqr( dummy_plug->get_dsqr() ); |
81 |
|
82 |
nConstrained++; |
83 |
constrained = 0; |
84 |
} |
85 |
} |
86 |
|
87 |
theArray = (SRI**) molecules[i].getMyBends(); |
88 |
for(int j=0; j<molecules[i].getNBends(); j++){ |
89 |
|
90 |
constrained = theArray[j]->is_constrained(); |
91 |
|
92 |
if(constrained){ |
93 |
|
94 |
dummy_plug = theArray[j]->get_constraint(); |
95 |
temp_con[nConstrained].set_a( dummy_plug->get_a() ); |
96 |
temp_con[nConstrained].set_b( dummy_plug->get_b() ); |
97 |
temp_con[nConstrained].set_dsqr( dummy_plug->get_dsqr() ); |
98 |
|
99 |
nConstrained++; |
100 |
constrained = 0; |
101 |
} |
102 |
} |
103 |
|
104 |
theArray = (SRI**) molecules[i].getMyTorsions(); |
105 |
for(int j=0; j<molecules[i].getNTorsions(); j++){ |
106 |
|
107 |
constrained = theArray[j]->is_constrained(); |
108 |
|
109 |
if(constrained){ |
110 |
|
111 |
dummy_plug = theArray[j]->get_constraint(); |
112 |
temp_con[nConstrained].set_a( dummy_plug->get_a() ); |
113 |
temp_con[nConstrained].set_b( dummy_plug->get_b() ); |
114 |
temp_con[nConstrained].set_dsqr( dummy_plug->get_dsqr() ); |
115 |
|
116 |
nConstrained++; |
117 |
constrained = 0; |
118 |
} |
119 |
} |
120 |
} |
121 |
|
122 |
if(nConstrained > 0){ |
123 |
|
124 |
isConstrained = 1; |
125 |
|
126 |
if(constrainedA != NULL ) delete[] constrainedA; |
127 |
if(constrainedB != NULL ) delete[] constrainedB; |
128 |
if(constrainedDsqr != NULL ) delete[] constrainedDsqr; |
129 |
|
130 |
constrainedA = new int[nConstrained]; |
131 |
constrainedB = new int[nConstrained]; |
132 |
constrainedDsqr = new double[nConstrained]; |
133 |
|
134 |
for( int i = 0; i < nConstrained; i++){ |
135 |
|
136 |
constrainedA[i] = temp_con[i].get_a(); |
137 |
constrainedB[i] = temp_con[i].get_b(); |
138 |
constrainedDsqr[i] = temp_con[i].get_dsqr(); |
139 |
} |
140 |
|
141 |
|
142 |
// save oldAtoms to check for lode balanceing later on. |
143 |
|
144 |
oldAtoms = nAtoms; |
145 |
|
146 |
moving = new int[nAtoms]; |
147 |
moved = new int[nAtoms]; |
148 |
|
149 |
prePos = new double[nAtoms*3]; |
150 |
} |
151 |
|
152 |
delete[] temp_con; |
153 |
} |
154 |
|
155 |
|
156 |
void Integrator::integrate( void ){ |
157 |
|
158 |
int i, j; // loop counters |
159 |
double kE = 0.0; // the kinetic energy |
160 |
double rot_kE; |
161 |
double trans_kE; |
162 |
int tl; // the time loop conter |
163 |
double dt2; // half the dt |
164 |
|
165 |
double vx, vy, vz; // the velocities |
166 |
double vx2, vy2, vz2; // the square of the velocities |
167 |
double rx, ry, rz; // the postitions |
168 |
|
169 |
double ji[3]; // the body frame angular momentum |
170 |
double jx2, jy2, jz2; // the square of the angular momentums |
171 |
double Tb[3]; // torque in the body frame |
172 |
double angle; // the angle through which to rotate the rotation matrix |
173 |
double A[3][3]; // the rotation matrix |
174 |
double press[9]; |
175 |
|
176 |
double dt = info->dt; |
177 |
double runTime = info->run_time; |
178 |
double sampleTime = info->sampleTime; |
179 |
double statusTime = info->statusTime; |
180 |
double thermalTime = info->thermalTime; |
181 |
|
182 |
double currSample; |
183 |
double currThermal; |
184 |
double currStatus; |
185 |
double currTime; |
186 |
|
187 |
int calcPot, calcStress; |
188 |
int isError; |
189 |
|
190 |
tStats = new Thermo( info ); |
191 |
e_out = new StatWriter( info ); |
192 |
dump_out = new DumpWriter( info ); |
193 |
|
194 |
Atom** atoms = info->atoms; |
195 |
DirectionalAtom* dAtom; |
196 |
dt2 = 0.5 * dt; |
197 |
|
198 |
// initialize the forces before the first step |
199 |
|
200 |
myFF->doForces(1,1); |
201 |
|
202 |
if( info->setTemp ){ |
203 |
|
204 |
tStats->velocitize(); |
205 |
} |
206 |
|
207 |
dump_out->writeDump( 0.0 ); |
208 |
e_out->writeStat( 0.0 ); |
209 |
|
210 |
calcPot = 0; |
211 |
calcStress = 0; |
212 |
currSample = sampleTime; |
213 |
currThermal = thermalTime; |
214 |
currStatus = statusTime; |
215 |
currTime = 0.0;; |
216 |
|
217 |
|
218 |
readyCheck(); |
219 |
|
220 |
#ifdef IS_MPI |
221 |
strcpy( checkPointMsg, |
222 |
"The integrator is ready to go." ); |
223 |
MPIcheckPoint(); |
224 |
#endif // is_mpi |
225 |
|
226 |
while( currTime < runTime ){ |
227 |
|
228 |
if( (currTime+dt) >= currStatus ){ |
229 |
calcPot = 1; |
230 |
calcStress = 1; |
231 |
} |
232 |
|
233 |
integrateStep( calcPot, calcStress ); |
234 |
|
235 |
currTime += dt; |
236 |
|
237 |
if( info->setTemp ){ |
238 |
if( currTime >= currThermal ){ |
239 |
tStats->velocitize(); |
240 |
currThermal += thermalTime; |
241 |
} |
242 |
} |
243 |
|
244 |
if( currTime >= currSample ){ |
245 |
dump_out->writeDump( currTime ); |
246 |
currSample += sampleTime; |
247 |
} |
248 |
|
249 |
if( currTime >= currStatus ){ |
250 |
e_out->writeStat( time * dt ); |
251 |
calcPot = 0; |
252 |
calcStress = 0; |
253 |
currStatus += statusTime; |
254 |
} |
255 |
|
256 |
#ifdef IS_MPI |
257 |
strcpy( checkPointMsg, |
258 |
"successfully took a time step." ); |
259 |
MPIcheckPoint(); |
260 |
#endif // is_mpi |
261 |
|
262 |
} |
263 |
|
264 |
dump_out->writeFinal(); |
265 |
|
266 |
delete dump_out; |
267 |
delete e_out; |
268 |
} |
269 |
|
270 |
void Integrator::integrateStep( int calcPot, int calcStress ){ |
271 |
|
272 |
// Position full step, and velocity half step |
273 |
|
274 |
//preMove(); |
275 |
moveA(); |
276 |
if( nConstrained ) constrainA(); |
277 |
|
278 |
// calc forces |
279 |
|
280 |
myFF->doForces(calcPot,calcStress); |
281 |
|
282 |
// finish the velocity half step |
283 |
|
284 |
moveB(); |
285 |
if( nConstrained ) constrainB(); |
286 |
|
287 |
} |
288 |
|
289 |
|
290 |
void Integrator::moveA( void ){ |
291 |
|
292 |
int i,j,k; |
293 |
int atomIndex, aMatIndex; |
294 |
DirectionalAtom* dAtom; |
295 |
double Tb[3]; |
296 |
double ji[3]; |
297 |
|
298 |
for( i=0; i<nAtoms; i++ ){ |
299 |
atomIndex = i * 3; |
300 |
aMatIndex = i * 9; |
301 |
|
302 |
// velocity half step |
303 |
for( j=atomIndex; j<(atomIndex+3); j++ ) |
304 |
vel[j] += ( dt2 * frc[j] / atoms[i]->getMass() ) * eConvert; |
305 |
|
306 |
// position whole step |
307 |
for( j=atomIndex; j<(atomIndex+3); j++ ) |
308 |
pos[j] += dt * vel[j]; |
309 |
|
310 |
|
311 |
if( atoms[i]->isDirectional() ){ |
312 |
|
313 |
dAtom = (DirectionalAtom *)atoms[i]; |
314 |
|
315 |
// get and convert the torque to body frame |
316 |
|
317 |
Tb[0] = dAtom->getTx(); |
318 |
Tb[1] = dAtom->getTy(); |
319 |
Tb[2] = dAtom->getTz(); |
320 |
|
321 |
dAtom->lab2Body( Tb ); |
322 |
|
323 |
// get the angular momentum, and propagate a half step |
324 |
|
325 |
ji[0] = dAtom->getJx() + ( dt2 * Tb[0] ) * eConvert; |
326 |
ji[1] = dAtom->getJy() + ( dt2 * Tb[1] ) * eConvert; |
327 |
ji[2] = dAtom->getJz() + ( dt2 * Tb[2] ) * eConvert; |
328 |
|
329 |
// use the angular velocities to propagate the rotation matrix a |
330 |
// full time step |
331 |
|
332 |
// rotate about the x-axis |
333 |
angle = dt2 * ji[0] / dAtom->getIxx(); |
334 |
this->rotate( 1, 2, angle, ji, &aMat[aMatIndex] ); |
335 |
|
336 |
// rotate about the y-axis |
337 |
angle = dt2 * ji[1] / dAtom->getIyy(); |
338 |
this->rotate( 2, 0, angle, ji, &aMat[aMatIndex] ); |
339 |
|
340 |
// rotate about the z-axis |
341 |
angle = dt * ji[2] / dAtom->getIzz(); |
342 |
this->rotate( 0, 1, angle, ji, &aMat[aMatIndex] ); |
343 |
|
344 |
// rotate about the y-axis |
345 |
angle = dt2 * ji[1] / dAtom->getIyy(); |
346 |
this->rotate( 2, 0, angle, ji, &aMat[aMatIndex] ); |
347 |
|
348 |
// rotate about the x-axis |
349 |
angle = dt2 * ji[0] / dAtom->getIxx(); |
350 |
this->rotate( 1, 2, angle, ji, &aMat[aMatIndex] ); |
351 |
|
352 |
dAtom->setJx( ji[0] ); |
353 |
dAtom->setJy( ji[1] ); |
354 |
dAtom->setJz( ji[2] ); |
355 |
} |
356 |
|
357 |
} |
358 |
} |
359 |
|
360 |
|
361 |
void Integrator::moveB( void ){ |
362 |
int i,j,k; |
363 |
int atomIndex; |
364 |
DirectionalAtom* dAtom; |
365 |
double Tb[3]; |
366 |
double ji[3]; |
367 |
|
368 |
for( i=0; i<nAtoms; i++ ){ |
369 |
atomIndex = i * 3; |
370 |
|
371 |
// velocity half step |
372 |
for( j=atomIndex; j<(atomIndex+3); j++ ) |
373 |
vel[j] += ( dt2 * frc[j] / atoms[i]->getMass() ) * eConvert; |
374 |
|
375 |
if( atoms[i]->isDirectional() ){ |
376 |
|
377 |
dAtom = (DirectionalAtom *)atoms[i]; |
378 |
|
379 |
// get and convert the torque to body frame |
380 |
|
381 |
Tb[0] = dAtom->getTx(); |
382 |
Tb[1] = dAtom->getTy(); |
383 |
Tb[2] = dAtom->getTz(); |
384 |
|
385 |
dAtom->lab2Body( Tb ); |
386 |
|
387 |
// get the angular momentum, and complete the angular momentum |
388 |
// half step |
389 |
|
390 |
ji[0] = dAtom->getJx() + ( dt2 * Tb[0] ) * eConvert; |
391 |
ji[1] = dAtom->getJy() + ( dt2 * Tb[1] ) * eConvert; |
392 |
ji[2] = dAtom->getJz() + ( dt2 * Tb[2] ) * eConvert; |
393 |
|
394 |
jx2 = ji[0] * ji[0]; |
395 |
jy2 = ji[1] * ji[1]; |
396 |
jz2 = ji[2] * ji[2]; |
397 |
|
398 |
dAtom->setJx( ji[0] ); |
399 |
dAtom->setJy( ji[1] ); |
400 |
dAtom->setJz( ji[2] ); |
401 |
} |
402 |
} |
403 |
|
404 |
} |
405 |
|
406 |
void Integrator::preMove( void ){ |
407 |
int i; |
408 |
|
409 |
if( nConstrained ){ |
410 |
if( oldAtoms != nAtoms ){ |
411 |
|
412 |
// save oldAtoms to check for lode balanceing later on. |
413 |
|
414 |
oldAtoms = nAtoms; |
415 |
|
416 |
delete[] moving; |
417 |
delete[] moved; |
418 |
delete[] oldPos; |
419 |
|
420 |
moving = new int[nAtoms]; |
421 |
moved = new int[nAtoms]; |
422 |
|
423 |
oldPos = new double[nAtoms*3]; |
424 |
} |
425 |
|
426 |
for(i=0; i<(nAtoms*3); i++) oldPos[i] = pos[i]; |
427 |
} |
428 |
} |
429 |
|
430 |
void Integrator::constrainA(){ |
431 |
|
432 |
int i,j,k; |
433 |
int done; |
434 |
double pxab, pyab, pzab; |
435 |
double rxab, ryab, rzab; |
436 |
int a, b; |
437 |
double rma, rmb; |
438 |
double dx, dy, dz; |
439 |
double rabsq, pabsq, rpabsq; |
440 |
double diffsq; |
441 |
double gab; |
442 |
int iteration; |
443 |
|
444 |
|
445 |
|
446 |
for( i=0; i<nAtoms; i++){ |
447 |
|
448 |
moving[i] = 0; |
449 |
moved[i] = 1; |
450 |
} |
451 |
|
452 |
|
453 |
iteration = 0; |
454 |
done = 0; |
455 |
while( !done && (iteration < maxIteration )){ |
456 |
|
457 |
done = 1; |
458 |
for(i=0; i<nConstrained; i++){ |
459 |
|
460 |
a = constrainedA[i]; |
461 |
b = constrainedB[i]; |
462 |
|
463 |
if( moved[a] || moved[b] ){ |
464 |
|
465 |
pxab = pos[3*a+0] - pos[3*b+0]; |
466 |
pyab = pos[3*a+1] - pos[3*b+1]; |
467 |
pzab = pos[3*a+2] - pos[3*b+2]; |
468 |
|
469 |
//periodic boundary condition |
470 |
pxab = pxab - info->box_x * copysign(1, pxab) |
471 |
* int(pxab / info->box_x + 0.5); |
472 |
pyab = pyab - info->box_y * copysign(1, pyab) |
473 |
* int(pyab / info->box_y + 0.5); |
474 |
pzab = pzab - info->box_z * copysign(1, pzab) |
475 |
* int(pzab / info->box_z + 0.5); |
476 |
|
477 |
pabsq = pxab * pxab + pyab * pyab + pzab * pzab; |
478 |
rabsq = constraintedDsqr[i]; |
479 |
diffsq = pabsq - rabsq; |
480 |
|
481 |
// the original rattle code from alan tidesley |
482 |
if (fabs(diffsq) > tol*rabsq*2) { |
483 |
rxab = oldPos[3*a+0] - oldPos[3*b+0]; |
484 |
ryab = oldPos[3*a+1] - oldPos[3*b+1]; |
485 |
rzab = oldPos[3*a+2] - oldPos[3*b+2]; |
486 |
|
487 |
rxab = rxab - info->box_x * copysign(1, rxab) |
488 |
* int(rxab / info->box_x + 0.5); |
489 |
ryab = ryab - info->box_y * copysign(1, ryab) |
490 |
* int(ryab / info->box_y + 0.5); |
491 |
rzab = rzab - info->box_z * copysign(1, rzab) |
492 |
* int(rzab / info->box_z + 0.5); |
493 |
|
494 |
rpab = rxab * pxab + ryab * pyab + rzab * pzab; |
495 |
rpabsq = rpab * rpab; |
496 |
|
497 |
|
498 |
if (rpabsq < (rabsq * -diffsq)){ |
499 |
#ifdef IS_MPI |
500 |
a = atoms[a]->getGlobalIndex(); |
501 |
b = atoms[b]->getGlobalIndex(); |
502 |
#endif //is_mpi |
503 |
sprintf( painCave.errMsg, |
504 |
"Constraint failure in constrainA at atom %d and %d\n.", |
505 |
a, b ); |
506 |
painCave.isFatal = 1; |
507 |
simError(); |
508 |
} |
509 |
|
510 |
rma = 1.0 / atoms[a]->getMass(); |
511 |
rmb = 1.0 / atoms[b]->getMass(); |
512 |
|
513 |
gab = diffsq / ( 2.0 * ( rma + rmb ) * rpab ); |
514 |
dx = rxab * gab; |
515 |
dy = ryab * gab; |
516 |
dz = rzab * gab; |
517 |
|
518 |
pos[3*a+0] += rma * dx; |
519 |
pos[3*a+1] += rma * dy; |
520 |
pos[3*a+2] += rma * dz; |
521 |
|
522 |
pos[3*b+0] -= rmb * dx; |
523 |
pos[3*b+1] -= rmb * dy; |
524 |
pos[3*b+2] -= rmb * dz; |
525 |
|
526 |
dx = dx / dt; |
527 |
dy = dy / dt; |
528 |
dz = dz / dt; |
529 |
|
530 |
vel[3*a+0] += rma * dx; |
531 |
vel[3*a+1] += rma * dy; |
532 |
vel[3*a+2] += rma * dz; |
533 |
|
534 |
vel[3*b+0] -= rmb * dx; |
535 |
vel[3*b+1] -= rmb * dy; |
536 |
vel[3*b+2] -= rmb * dz; |
537 |
|
538 |
moving[a] = 1; |
539 |
moving[b] = 1; |
540 |
done = 0; |
541 |
} |
542 |
} |
543 |
} |
544 |
|
545 |
for(i=0; i<nAtoms; i++){ |
546 |
|
547 |
moved[i] = moving[i]; |
548 |
moving[i] = 0; |
549 |
} |
550 |
|
551 |
iteration++; |
552 |
} |
553 |
|
554 |
if( !done ){ |
555 |
|
556 |
sprintf( painCae.errMsg, |
557 |
"Constraint failure in constrainA, too many iterations: %d\n", |
558 |
iterations ); |
559 |
painCave.isFatal = 1; |
560 |
simError(); |
561 |
} |
562 |
|
563 |
} |
564 |
|
565 |
void Integrator::constrainB( void ){ |
566 |
|
567 |
int i,j,k; |
568 |
int done; |
569 |
double vxab, vyab, vzab; |
570 |
double rxab, ryab, rzab; |
571 |
int a, b; |
572 |
double rma, rmb; |
573 |
double dx, dy, dz; |
574 |
double rabsq, pabsq, rvab; |
575 |
double diffsq; |
576 |
double gab; |
577 |
int iteration; |
578 |
|
579 |
for(i=0; i<nAtom; i++){ |
580 |
moving[i] = 0; |
581 |
moved[i] = 1; |
582 |
} |
583 |
|
584 |
done = 0; |
585 |
while( !done && (iteration < maxIteration ) ){ |
586 |
|
587 |
for(i=0; i<nConstrained; i++){ |
588 |
|
589 |
a = constrainedA[i]; |
590 |
b = constrainedB[i]; |
591 |
|
592 |
if( moved[a] || moved[b] ){ |
593 |
|
594 |
vxab = vel[3*a+0] - vel[3*b+0]; |
595 |
vyab = vel[3*a+1] - vel[3*b+1]; |
596 |
vzab = vel[3*a+2] - vel[3*b+2]; |
597 |
|
598 |
rxab = pos[3*a+0] - pos[3*b+0];q |
599 |
ryab = pos[3*a+1] - pos[3*b+1]; |
600 |
rzab = pos[3*a+2] - pos[3*b+2]; |
601 |
|
602 |
rxab = rxab - info->box_x * copysign(1, rxab) |
603 |
* int(rxab / info->box_x + 0.5); |
604 |
ryab = ryab - info->box_y * copysign(1, ryab) |
605 |
* int(ryab / info->box_y + 0.5); |
606 |
rzab = rzab - info->box_z * copysign(1, rzab) |
607 |
* int(rzab / info->box_z + 0.5); |
608 |
|
609 |
rma = 1.0 / atoms[a]->getMass(); |
610 |
rmb = 1.0 / atoms[b]->getMass(); |
611 |
|
612 |
rvab = rxab * vxab + ryab * vyab + rzab * vzab; |
613 |
|
614 |
gab = -rvab / ( ( rma + rmb ) * constraintsDsqr[i] ); |
615 |
|
616 |
if (fabs(gab) > tol) { |
617 |
|
618 |
dx = rxab * gab; |
619 |
dy = ryab * gab; |
620 |
dz = rzab * gab; |
621 |
|
622 |
vel[3*a+0] += rma * dx; |
623 |
vel[3*a+1] += rma * dy; |
624 |
vel[3*a+2] += rma * dz; |
625 |
|
626 |
vel[3*b+0] -= rmb * dx; |
627 |
vel[3*b+1] -= rmb * dy; |
628 |
vel[3*b+2] -= rmb * dz; |
629 |
|
630 |
moving[a] = 1; |
631 |
moving[b] = 1; |
632 |
done = 0; |
633 |
} |
634 |
} |
635 |
} |
636 |
|
637 |
for(i=0; i<nAtoms; i++){ |
638 |
moved[i] = moving[i]; |
639 |
moving[i] = 0; |
640 |
} |
641 |
|
642 |
iteration++; |
643 |
} |
644 |
|
645 |
if( !done ){ |
646 |
|
647 |
|
648 |
sprintf( painCae.errMsg, |
649 |
"Constraint failure in constrainB, too many iterations: %d\n", |
650 |
iterations ); |
651 |
painCave.isFatal = 1; |
652 |
simError(); |
653 |
} |
654 |
|
655 |
} |
656 |
|
657 |
|
658 |
|
659 |
|
660 |
|
661 |
|
662 |
|
663 |
void Integrator::rotate( int axes1, int axes2, double angle, double ji[3], |
664 |
double A[3][3] ){ |
665 |
|
666 |
int i,j,k; |
667 |
double sinAngle; |
668 |
double cosAngle; |
669 |
double angleSqr; |
670 |
double angleSqrOver4; |
671 |
double top, bottom; |
672 |
double rot[3][3]; |
673 |
double tempA[3][3]; |
674 |
double tempJ[3]; |
675 |
|
676 |
// initialize the tempA |
677 |
|
678 |
for(i=0; i<3; i++){ |
679 |
for(j=0; j<3; j++){ |
680 |
tempA[j][i] = A[i][j]; |
681 |
} |
682 |
} |
683 |
|
684 |
// initialize the tempJ |
685 |
|
686 |
for( i=0; i<3; i++) tempJ[i] = ji[i]; |
687 |
|
688 |
// initalize rot as a unit matrix |
689 |
|
690 |
rot[0][0] = 1.0; |
691 |
rot[0][1] = 0.0; |
692 |
rot[0][2] = 0.0; |
693 |
|
694 |
rot[1][0] = 0.0; |
695 |
rot[1][1] = 1.0; |
696 |
rot[1][2] = 0.0; |
697 |
|
698 |
rot[2][0] = 0.0; |
699 |
rot[2][1] = 0.0; |
700 |
rot[2][2] = 1.0; |
701 |
|
702 |
// use a small angle aproximation for sin and cosine |
703 |
|
704 |
angleSqr = angle * angle; |
705 |
angleSqrOver4 = angleSqr / 4.0; |
706 |
top = 1.0 - angleSqrOver4; |
707 |
bottom = 1.0 + angleSqrOver4; |
708 |
|
709 |
cosAngle = top / bottom; |
710 |
sinAngle = angle / bottom; |
711 |
|
712 |
rot[axes1][axes1] = cosAngle; |
713 |
rot[axes2][axes2] = cosAngle; |
714 |
|
715 |
rot[axes1][axes2] = sinAngle; |
716 |
rot[axes2][axes1] = -sinAngle; |
717 |
|
718 |
// rotate the momentum acoording to: ji[] = rot[][] * ji[] |
719 |
|
720 |
for(i=0; i<3; i++){ |
721 |
ji[i] = 0.0; |
722 |
for(k=0; k<3; k++){ |
723 |
ji[i] += rot[i][k] * tempJ[k]; |
724 |
} |
725 |
} |
726 |
|
727 |
// rotate the Rotation matrix acording to: |
728 |
// A[][] = A[][] * transpose(rot[][]) |
729 |
|
730 |
|
731 |
// NOte for as yet unknown reason, we are setting the performing the |
732 |
// calculation as: |
733 |
// transpose(A[][]) = transpose(A[][]) * transpose(rot[][]) |
734 |
|
735 |
for(i=0; i<3; i++){ |
736 |
for(j=0; j<3; j++){ |
737 |
A[j][i] = 0.0; |
738 |
for(k=0; k<3; k++){ |
739 |
A[j][i] += tempA[i][k] * rot[j][k]; |
740 |
} |
741 |
} |
742 |
} |
743 |
} |